<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Juntao,<div class=""><br class=""></div><div class=""> The error is not related to whether your sequences form a complex. It is simply a bug or limitation of AlphaFold that is causing the failure. There are many bugs in AlphaFold that can cause this. To figure out which one you are hitting you should look in the log file that the error message lists. If ChimeraX downloaded the results (I think it will even if all 5 predictions give errors) then they will be on your computer in</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>~/Downloads/ChimeraX/AlphaFold/prediction_1</div><div class=""><br class=""></div><div class="">and the errors for each prediction will be in files model_1_error, model_2_error...</div><div class=""><br class=""></div><div class=""> If you send that error log file I can probably tell you what the cause is. Sometimes it is CUDA is out of memory (GPU does not have enough memory) -- common if your total sequence length is > 1000 amino acids. But other failures happen, e.g. in energy minimization. If the problem is the sequence length is too long, then you should try to run AlphaFold on your own computers with a modern GPU with lots of memory instead of Google Colab which uses 5 year old GPUs with only 16 Gbytes of memory.</div><div class=""><br class=""></div><div class=""> Here are some test runs of AlphaFold giving you some examples of the kinds of failures that occur.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html" class="">https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 14, 2022, at 10:09 AM, Juntao Yu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear ChimeraX community,<div class=""><br class=""></div><div class="">I am a graduate student from Harvard Medical School who recently became interested in using AlphaFold-Multimer to predict protein complex structures of my interest. I have been tried a few times of predicting one protein complex and I was able to finish all MSA. However, when AlphaFold starts predicting the structure, all five models were reported as “error”. It is surprising to me because it is known that these two proteins should form a complex. I noticed in the script on the line is: “<span style="font-family: monospace, Menlo, Monaco, "Courier New", monospace; font-size: 14px; white-space: pre; background-color: rgb(255, 255, 254);" class="">print (</span><span style="font-family: monospace, Menlo, Monaco, "Courier New", monospace; font-size: 14px; white-space: pre; color: rgb(163, 21, 21);" class="">'\nAlphaFold generated an error computing %s, error logged to %s\n'</span><span style="font-family: monospace, Menlo, Monaco, "Courier New", monospace; font-size: 14px; white-space: pre; background-color: rgb(255, 255, 254);" class="">% (model_name, error_log_path))</span>”. The results printed exactly what this line says. </div><div class=""><br class=""></div><div class="">I am wondering whether it means the Multimer is not able to predict this complex structure? Is there any tutorial that I can find to change parameters in order to try to improve and get a structure?</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Juntao</div><div class=""><br class=""></div><div class="">------------------------------------------</div><div class=""><b style="caret-color: rgb(0, 0, 0); font-family: Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Juntao Yu | Ph.D. candidate</b><div style="caret-color: rgb(0, 0, 0); font-family: Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Moazed Lab<br class="">Department of Cell Biology<br class="">Harvard Medical School</div><div style="caret-color: rgb(0, 0, 0); font-family: Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">240 Longwood Avenue<br class="">Boston, MA 02115</div>
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